References in additional includes cannot be found

[yakatz]

I am not totally sure if this is Pandoc or an extension

I need to change the way appendix chapters are numbers to meet style rules. I copied the built-in tex template and added the following at the end:

$body$

\chapterstyle{myappendix}
\renewcommand{\chaptername}{Appendix}
\renewcommand{\thechapter}{\Alph{chapter}}
%\cftaddtitleline{toc}{chapter}{Appendices}{}
\appendix
\addtocontents{toc}{\protect\setcounter{tocdepth}{0}}

$for(include-after)$
$include-after$

$endfor$
\backmatter

\end{document}

In my main md file, I have this:

---
... other metadata ...
include-after: |
  ``` {.include shift-heading-level-by=-1}
  back-pages/1-appendix_a.md
  back-pages/2-appendix_b.md
  back-pages/3-appendix_c.md
  ```
---

``` {.include}
chapters/1-intro.md
...
chapters/99-conclusion.md
```

The back pages are included and the table of contents is properly built, but I can't add references to the contents of the appendices (although I can add references to the chapter titles).

Example appendix contains

# `myprogram` Code Listing {#sec:a_coderef}

This is the code listing for the program...
...

![Control Flow Graph for `myprogram`](../visio_export/CFG - Basic - labeled.png){#fig:simple_cfg_a width=95%}

Works: A code listing for `myprogram` with cross-references to its Configuration Flow Graph is in [appendix @sec:a_coderef].

Doesn't work: In the Control Flow Graph in [figure @fig:simple_cfg_a], 

Command
pandoc --template=template-mytemplate.tex --lua-filter=tools/include-files.lua --lua-filter=tools/alignment.lua --filter=pandoc-crossref --citeproc --lua-filter=tools/text-crossrefs.lua --lua-filter=tools/short-captions.lua --standalone --pdf-engine=xelatex -N --highlight-style=haddock -o mypaper.pdf mypaper.md

include-files.lua is from here: https://github.com/pandoc-ext/include-files/blob/c86e823ad6e40c594d7b5c83166271703d2d49b7/include-files.lua

Pandoc version?
Windows 11
pandoc.exe 3.2.1

[jgm]

citeproc only runs over the document's body, so it won't affect things you put in include-after.

Since pandoc can pass through raw latex content in a markdown file, you could just put this at the beginning of your first appendix file.

```{=latex}
\chapterstyle{myappendix}
\renewcommand{\chaptername}{Appendix}
\renewcommand{\thechapter}{\Alph{chapter}}
%\cftaddtitleline{toc}{chapter}{Appendices}{}
\appendix
\addtocontents{toc}{\protect\setcounter{tocdepth}{0}}
```

And then put the appendix files on the command line as arguments, after mypaper.md.

[yakatz]

My final main md file looks like this:

``` {.include}
chapters/1-intro.md
...
chapters/99-conclusion.md
```

``` {.include}
back-pages/0-appendix_meta.md
back-pages/1-appendix_a.md
back-pages/2-appendix_b.md
back-pages/3-appendix_c.md
```

To make the table of contents work, I also had to go back to my template tex and remove all the other plumbing I had put in for the include-after, i.e:

-$if(include-after)$
 \renewcommand\cftappendixname{\appendixname~}
-$endif$